The Dark Time
by Serpent Magick
Summary: Super!hiatus. If it's continued, it'll be a rewrite.
1. Chapter 1

**Disclaimer:** I don't own pokemon, but all _my_ characters are _mine._

**A/N: **A couple days ago my muse suddenly smacked me over the head and said "Write this!". "But I have others to work on! Why a new one?" I asked hesitantly. "Just do it!" she screamed in my ear, reminding me very much of Navi...

/-/-/-/-/

It was a scary time to be alive, it truly was. The threat of Team Rocket was everywhere; it got to the point where people could no longer trust their own family members. It was bad to be caught out alone, even worse at night. Only the foolish or the desperate ever did that. Once the Rockets had their sights on you, there was no escaping…ever. Sometimes people would just…disappear…

/-/-/-/-/

Ayla was running through the darkness, occasionally stumbling in the thick grass. Her Togetic was floating slightly behind her, clutching her white-streaked blonde hair. He was worried about his friend; after the Rockets had come for her a few weeks ago she hadn't been well. They left her Celadon home quickly, and since then her health had gone into a downward spiral, the stress prematurely whitening her hair and making her weak.

Her amber eyes no longer shone, dully reflecting the moonlight as she fought her way through the woods. They were probably near Pewter City by now; she ran to her relative's house. They would hide her, they had to. Her parents had left her; they had disappeared a few years ago when she was fifteen. Now at seventeen, she had supported herself by working in the Department Store, but before that her aunt and uncle took care of her in Pewter City.

She could no longer keep running, and fell panting and sobbing on the damp ground, her already dirty clothes becoming muddier. Togetic sadly floated to her face, stroking her cheek in the hopes of calming his friend. He had been a gift from her parents as a Togepi when she was twelve, but Ayla wasn't really a trainer; he was more like a companion to her and was treated like a dear friend. Needless to say, it took him little time to evolve.

Ayla eventually started to calm, and as she regained her breath she stood. Steadying herself on her weak legs she continued on at a hurried pace, holding Togetic to her chest and seeming to draw strength from his closeness. Her pale complexion stood out in the dark woods, making her look like a ghost drifting through the trees.

The few minutes of quiet ended too quickly. Soon the duo could hear trudging footsteps behind them, and the low buzz of far-off conversation. Togetic picked up on the ill will they gave off and warned Ayla with a frantic but quiet cry. The malnourished seventeen year old took off running, trying as hard as she could to make as little noise as possible, but to little avail.

The sounds of pursuit could be heard; the eerie howls of the tracking Houndour and the screeches of Sneasel were the most prominent in the cacophony of noise. Team Rocket had apparently picked up some new pokémon.

Ayla gave out a distressed cry as she caught her foot on a root and tumbled to the ground, instinctually falling on her side to avoid landing on Togetic. She scrambled to her feet but it was already too late; in just that moment she had fallen, the Houndour caught up. There were three of them, all bearing their fangs and growling viciously at her. She edged backwards towards the woods but found her path blocked by a vicious looking Sneasel.

Togetic could no longer bear to let his friend be scared and jumped forward in a battle stance, drawing the other pokémon's attention form Ayla. He looked back at her and nodded, saying without words that he would battle. Ayla too nodded and gave her first order.

"Use Ancientpower, my friend!" she called as strongly as her voice would allow.

Togetic glowed faintly, and suddenly a line of boulders appeared out of the ground. They flew at the Houndour, hitting two of them. One was trapped below the large boulders and moved no more, a puddle of crimson slowly seeping into the ground around it. The other two Houndour, as well as the Sneasel retaliated by viciously biting and scratching Togetic.

"Togetic, try Metronome!" Ayla called frantically, knowing that she was taking a big chance. Luckily for them, the move was in their favor.

Togetic jumped into the air, and then slammed back down with great power; a powerful Earthquake tore the ground. The remaining Houndour took great damage, but the Sneasel had jumped at just the right moment to avoid the attack completely. Without orders, Togetic tried to Charm the Sneasel, but it resisted and attacked with a devastating Slash.

Togetic fell to the ground with a weak cry, its face and neck torn open by the sharp clawed pokémon. Ayla ran to her fallen friend and scooped him up into her arms, trying desperately to stop the flow of blood from the horrific wound.

The Rocket pokémon continued to attack, not seeming to care that they were now hitting the human and not the Togetic. Ayla did her best to shield her friend from the hits, curling around him to that she took the damage instead. She sobbed to herself, more because she could feel her companion's blood soaking her front than the wounds being inflicted on her.

Togetic knew that he was going to die; not even a Wish could save him now…but maybe it could save Ayla. He started chanting quietly to the heavens, Wishing with all his might that his friend would be spared from the clutches of death. He poured the rest of his life's power into that one Wish, with all his Heart and Soul wanting his friend to live…

Ayla started to sob harder when she felt Togetic's breathing go shallow, his small body still against her chest. She felt cold, but was unsure if it was from loss of her friend, or the loss of blood because of the grievous wounds covering her back. She knew that soon the Rockets would arrive and take her away…and that scared her more than death itself.

She noticed distantly that the pokémon had stopped attacking, and weakly opened her eyes. What she saw confused her greatly: surrounding her was a large pink bubble, and the other pokémon appeared to not be able to get to her. It was then that the tingling started. From the top of her head, to the tips of her fingers and toes, she felt an odd tingling sensation. It was the kind of familiar not-pain that was associated with your hand or foot falling asleep, only this was over her whole body.

It was suddenly when a sharp pain hit her in the abdomen, and it felt like her organs were simultaneously liquefying. She cried out in pain, and started to scream before she was suddenly cut off by her body convulsing. Her body no longer felt solid; everything beneath her tingling skin felt like jelly. Her bones started to shrink and reform, her skin doing the same, her organs then reforming from the jelly to fit the new body shape.

Ayla curled into the fetal position whimpering, blood coming out of her mouth from where she had bitten her tongue, even as her face reshaped itself. Her eye sockets became larger, her eyes following suit underneath the tightly clinched eyelids. Her jaw and nose shrank into her face, and then reformed as a muzzle that seemed to hide her new mouth. Her ears too shrank into her skull, reappearing in the shape of triangles at the top of her head.

She faintly cried out as a long tail formed from the base of her spine, eventually becoming twice the length of her small body. Pops continued to issue from her now vaguely feline form as the bones each fit into place, Ayla shuddering in turn.

There was a brief pause before fine fur started to grow, her body turning such a light pink that it looked white. As the wave of fur reached her triangular ears, long back feet, and even longer tail it turned to a darker pink, almost purple at the very tips.

Ayla shuddered, expecting more pain, but finding none forthcoming. She opened her (very large) amber eyes and looked around, noticing that the bubble was still around her and the Rocket pokémon were staring at her in shock. Ignoring them, she crawled over to Togetic's body, which was now larger than she was. She turned her friend's head towards her with her petite paw, grimacing as she saw the pained look on his face. His eyes still glimmered slightly, and his mouth formed as small smile, but even as she watched the sparkle in his eye disappeared forever.

She lay her head on his still chest, crying against the soft down that covered his body, slightly sticky with his blood. With her head buried in his chest, she didn't notice when her shield flickered and died, so it came as a shock to her when she was suddenly tackled into a tree.

Gasping for breath she watched as the Rocket pokémon approached her; all of them had their fangs bared and looked ready to eat her alive. They probably would have, if their trainers hadn't come in at that moment. Ayla couldn't help but feel an odd mix of thankfulness and hate at the same time.

It looked as if they had been about to say something, but as soon as the group of Rockets saw her, they fell silent. They didn't appear to notice that one Houndour lay dead beneath a boulder, or the cries of their pokémon trying to tell them what happened, instead fully focused on the small pink pokémon at the base of a tree. They stood very still, and when it appeared that Ayla would not move, they sprang into action.

It wouldn't matter that the girl they had been tracking got away when they presented a Legend to the Boss. Greed shone in their eyes as they surrounded her, wicked smiles on their faces as they seemed to pull a net out of thin air.

Ayla lunged over to Togetic's body, holding tight to her deceased partner even as one of the Rockets grabbed her tail and pulled hard. She let out a pitiful wail as they tore her away from the body, kicking anyone who came close to her. She continued to wail and struggle as they forced her into a net bag that was lined with some sort of sticky substance, probably meant to keep her in.

The Dark pokémon just stood back quietly as their masters trapped the newly transformed Mew, looking a little nervous and confused. Ayla tried to appeal to them, calling out for help, but they averted their gazes to the ground and continued to ignore her. While she thrashed about in the mesh bag, one of the Rockets said something over the radio, and in a little less than a minute a chopper appeared overhead, blowing leaves and dirt around viciously.

The Rockets returned their pokémon and loaded into the chopper, being careful to keep a firm hold on Ayla's net. There was no way they would lose this pokémon because of a stupid mistake. The Mew had all but given up on escaping, her feet dangling listlessly through the holes in the net and she laid her head against the strong rope. Exhausted from her transformation, she didn't struggle anymore, her eyes fading as she watched the white and crimson spot outside the helicopter, where her friend lay.

Darkness enveloped the small pokémon as the Rockets carefully placed her into a strong black box, not even bothering to take her out of the net first.

As the whirring sound of the chopper finally faded away, the clearing was again free of activity. All that lay there now was a line of boulders, the limbs of a Houndour protruding from underneath one, a dead but peaceful looking Togetic, and a pile of tattered clothes.

In the dark sky above, a single star shone brighter than the others. Togetic's Wish had been fulfilled, for better or worse.

/-/-/-/-/

**A/N: I'm not quite sure what the rating should be...could you guys help me?** **I need to know if it should be in M. **This will be a very dark fic at times, just so you know. /smacked over head by muse/ Uhm, could you leave a review.../whispers/ she's gonna kill me, please feed her...


	2. Chapter 2

**Disclaimer: **Nope, don't own Pokemon. My characters and plot belong to me though.

**A/N:** Wow, I really wasn't expecting that many reviews just for the first chapter! Not that I'm complaining, mind you, I actually wanna thank you guys for reviewing. I hope you all enjoy this one; insight into the past.

/-/-/-/-/

A small group of people stood quietly around a tube-like tank, observing its contents with wonder. Floating somewhere near the center of the tank, with multiple wires attached to check vital signs, was a small pinkish-white pokémon; one many still considered a myth. Mew was in their possession at last…who cared about fossilized remains when they had the living, breathing, pokémon itself?

Giovanni would be very pleased.

Inside the tank, the small creature stirred in her slumber.

/-/-/-/-/

_**(Age 12)**_

_Ayla looked curiously to her parent's smiling faces. In her mother's arms was a small pokémon, looking at her curiously with its cute baby face._

_"It's a Togepi, dear," her mother said as she handed her daughter the baby pokémon._

_"Happy birthday, Ayla." They said together as she cradled the happy pokémon, holding it close and laughing gleefully._

_"We'll be friends forever!" Ayla sang to Togepi._

_**(Age 13)**_

_"C'mon Togepi, we've gotta take the groceries in for Mom," Ayla called to her friend, currently following closely behind her. He couldn't really help carry the groceries, but he always went everywhere with Ayla._

_Everything seemed to move in slow-motion for a few seconds; right as Ayla reached for the bags sitting on the steps before her, a figure passed by. As they passed Ayla let out a startled squeak as the person grabbed the wallet out of her back pocket and ran._

_"Hey you, get back here!" she called angrily, scooping Togepi up into her arms (out of reflex) and giving chase. _

_Togepi could feel Ayla's heart beating a frantic rhythm as she sprinted down the sidewalk after the thief. She turned sharply into an alley and her foot got caught on the treacherous junk lying around. She cried out in pain and immediately grabbed her twisted ankle, rocking back and fourth on the dirty pavement. She tried to stand after a moment, but had little success and slumped against the wall._

_She sighed and held Togepi a little closer; it was getting dark now, and she was scared to be outside alone. Celadon wasn't really the safest place to be at night…especially injured…_

_Togepi made up his mind. He struggled out of his friend's arms and turned to face her. In answer to her hurt and questioning gaze, he pointed in the direction of their apartment. She had the curious look on her face for a moment more before realizing that he was going to get her parents. As he set off towards home, he faintly heard her murmur something._

"_Please hurry," she said, mostly to herself, as she delicately held her swelling ankle._

_Togepi moved as quickly as he could towards home, but tripped often on the creepily barren sidewalk. It seemed that Ayla wasn't the only person who thought it bad to be outside after dark. The sun was rapidly sinking below the horizon, creating a beautiful array of colors that he had no time to watch. He tried to move faster, but that was one thing his body was not built for, and he often fell. Togepi started to panic as the shadows started to cover more and more of the city; he wasn't even halfway there yet! There was no way he would make it there and back before something bad happened to Ayla; he needed to protect his friend!_

_Suddenly a tingling energy overcame Togepi. He felt his body becoming more slim and taller, giving him more mobility. Two wings appeared on his back, although he knew immediately that he only needed them to change direction, as he was already floating about a foot above the ground without even moving them. Now a Togetic, and brimming with evolution energy, it took him practically no time to reach their apartment._

_In only a few short minutes he had convinced Ayla's parents to come, and he was reunited with his grateful friend._

_"Togepi," she giggled "I mean Togetic, thank you!" Ayla said, tears glistening in her amber eyes as she hugged her companion._

_**(Age 14)**_

_Ayla and Togetic were playing just outside Celadon, in the fields between Saffron and Celadon cities called Route 7. They were playing a mix of tag, and hide-and-seek. It seemed that Togetic had the advantage, because he often flew high enough to pick out his companion from her hiding spot. Ayla, though, had speed, and as soon as she saw Togetic approaching she would bolt, her blonde hair streaming out behind her as she laughed._

_It was in one of those sporadic moments of rest between their games that, as they lay laughing on the ground, they were approached by a cautious pokémon. Having seen the fun the duo was having, the fox pokémon Vulpix carefully walked out of the grass, watching them curiously, its brilliant red-orange fur shining silkily in the sun._

_Togetic having warned her of their visitor, Ayla rolled onto her stomach and faced the Vulpix, somewhat startling the fox. Ayla chuckled lightly and invited the fire fox over, holding out her hand in invitation. Togetic chirped in too, inviting it over to play with them._

_Vulpix happily bound over and, giving the offered hand a lick, then proceeded to tackle Togetic to the ground in a friendly manner. They laughed and rolled around for a few minutes, while Ayla watched them with a small smile on her face. They all played in that field for hours, until it was dark and the duo had to leave. They promised to meet the next day in the same spot to play._

_Every day after that Ayla and Togetic met up with Vulpix on Route 7 to play. Some days they would simply play, and some they would have picnics. But they all had fun._

_This was a beacon of light in the increasingly dark times._

_**(Age 15)**_

_Ayla had just gotten home from her part-time job at the nearby Department Store and, dropping her bag by the door, started on dinner. Her parents wouldn't be home for another hour or so; they both had full time jobs, her mother working at a pokémon salon, and her father working at the Game Corner. Since Ayla always got home first, she usually cooked them all dinner, Togetic never leaving her side._

_She finally finished cooking the chicken and dumplings (giving Togetic a dumpling, which he happily chirped at receiving) and looked to see the time. _

_"Odd," she said to Togetic "They're usually home by now, it's almost 5:30."_

_Togetic continued eating his dumpling, but floated up next to Ayla and landed on her shoulder, reassuring her._

_When the clock reached 6 o'clock and Ayla still hadn't heard anything from her parents she donned a light jacked and was about to leave the house, when the phone rang. She jumped slightly at the noise and hurried over to the table it sat on: when she noticed that the caller-id read "Mom's cell" she hurriedly picked it up._

_"Where are you Mom, dinner's already getting cold—" She was cut off by the frantic voice of her mother on the other end of the receiver. _

_"Listen to me Ayla, this is important!" she spoke quickly and sounded hysterical "Your father and I were abducted on out way home…I…I think it's Team Rocket,"_

_"Mom! No! Where are you, I can get the police—I" Ayla called back frantically, earning her a concerned look from Togetic._

_"No, we've already decided, you have to go to your Aunt and Uncle in Pewter City. You can't help us, just run. There's money in on the dresser in our bedroom; it should be enough to get a Pidgeot flight to Pewter. Just get out of Celadon before they come for you—" She was suddenly cut off, and Ayla heard a voice in the background._

_"Who the hell's on the line?! Give me that phone you bitch!" A harsh voice yelled, and then the line when dead. _

_Ayla went cold and dropped the phone. Togetic immediately floated over and asked without words what was wrong. Ayla shook her head and snapped out of it, immediately heading towards her parent's bedroom._

_"Togetic, could you pack up the dumplings? We need to leave now to go stay with my Aunt and Uncle," Her voice was shaking slightly, but she tried to stay calm at least until she got out of the city. Togetic nodded, but stayed floating in place until Ayla turned away and continued into the bedroom. _

_Ayla faintly heard rustling in the kitchen as Togetic packed the dumplings into a lined lunchbox. She hurried over to the hardwood dresser that sat up against the far wall of her parent's bedroom. Almost immediately she saw a small box sitting far against the wall on the dresser, and inside was a rather large wad of money. Ayla didn't bother counting it as she shoved it deep into the pocket of her jeans._

_Next she moved onto her room, grabbing another backpack and throwing some of her clothes into in haphazardly. She didn't bother taking much else, but paused as she was at the door. Turning back she grabbed a framed picture of her parents and herself at a festival in Saffron and stuffed it into the backpack as well._

_When she emerged back out into the kitchen, she immediately saw Togetic floating about her eye level, holding the lunchbox. He had a worried look on his face, and it grew more so when he saw the backpack on her shoulders. Ayla took the lunchbox with a weak smile._

_"We need to leave, Togetic," she said, her eyes growing watery from unshed tears "Team Rocket has Mom and Dad…t-they want us to leave so we're out of danger." A tear finally fell from her eye, trickling down her cheek._

_Togetic floated closer and wiped the tear away, trying to calm his friend, even if he himself was worried as well. Team Rocket was growing more and more open about their activities, so much in fact, that even the wild pokémon were aware of the changes in the human world._

_"Come on, Togetic. We have to leave now," Ayla beckoned him out the door, and she locked it behind them, tucking the key into her backpack._

_They reached the area where one could rent out a flying pokémon to take them to other towns relatively quickly. They encountered no problems, and Ayla paid for the Pidgeot flight to Pewter._

_The flight passed in respective silence, Togetic tucked sleeping in the backpack while Ayla shed silent tears high above the ground._

_**(Age 16)**_

_"Are you sure you're ready to leave?" Ayla's Aunt asked, somewhat worriedly. Her Uncle stood quietly behind her, a comforting hand on her shoulder. Togetic sat on her opposite shoulder, again looking at her in a concerned manner. They had been doing that more and more since her parents had gone…_

_"As ready as I'll ever be," she mumbled under her breath, so only Togetic could hear. "Yes, I think I'm ready to go back to Celadon now," she said louder, so her Aunt and Uncle could hear. She had already packed her meager belongings into the backpack she initially brought with her. _

_They had been very nice to her over the time she had spent at their home, about a year, actually. She wasn't the closest to them, but they invited her into their home and helped her as much as they could. When she had told them a few days ago that she wanted to go back to Celadon, they had been a little surprised, but didn't try to stop her. She was old enough to make her own way in life._

_"Here, at least let Aerodactyl take you back," her Uncle insisted, releasing the grayish-purple Fossil pokémon. It happily nuzzled against Ayla's hand; the two had gotten to be friends over her extended stay. She smiled faintly and pet the pokémon on the head, before climbing on its back. _

_Not one for long goodbyes, Ayla simply waved to them as Aerodactyl took flight. Watching the scenery pass below them (and noting Aerodactyl was faster than the Pidgeot had been) she wondered if she could get her job back at the Department Store…_

_**(Age 17, about 3 weeks previous of the Change)**_

_Another day working at the Department Store, it wasn't a busy one either. Ayla sighed dully at the counter as Togetic shuffled around behind her. After the manager had heard about her parents, they had decided to let Ayla bring Togetic with her. After all, they were a store for trainers mostly; perhaps a pokémon would boost business._

_With nothing better to do, Ayla opened the case containing evolution stones and started to polish them: the perks about working on the fourth floor. You didn't have to be constantly bothered like in the general shops, only people with money to spare could buy evolution stones. There were also pokémon dolls…but no one but collectors really bought them._

_Satisfied with her work, Ayla held the fire stone out before her. It shone a vibrant orange, its core color a deep red. Ayla narrowed her eyes slightly when she noticed in the reflection that someone was approaching the counter. She placed the stone back in its case and turned towards the customer, plastering a fake smile on her face. A nondescript male was standing at the counter; the only thing making him stand out was a rather cold look in the eyes._

_"How may I help you, sir?" Ayla asked as politely as she could, as was required by her job. "Are you interested in our high quality evolution stones? Or perhaps the new shipment of pokémon doll we just got in," she gestured to the shelf behind her, containing a wide array of cute dolls._

_"Actually," he said quietly "I'm looking for someone," he looked her in the eyes "And I believe you know where I can find her, don't you Ayla."_

_Ayla's blood seemed to run cold, she recognized that voice, even after more than two years. It sounded just like the voice she had heard over the phone, when her parents were taken…that would make him…_

_"Yes, stay quite Ayla," he chuckled. It was all just a joke to him; was all of Team Rocket this cruel?_

_Togetic, sensing Ayla's distress, attacked the Rocket member, using a strong Double-Edge and knocking him into the shelves containing a large amount of magazines. Ayla would have cringed, knowing it was her job to prevent messes, but she wasn't thinking about work anymore: she knew that she and Togetic had to get away now._

_"Togetic, come on! We've gotta go!" Ayla shouted as she ran from behind the counter. The Rocket member was starting to get to his feet, but she gave him a solid kick in the stomach to buy more time._

_Ayla and Togetic hurried out of the Department Store, drawing many curious glances along the way. They didn't stop by her apartment to grab anything, or go to the Pidgeot flight-point. Ayla was sure that if Team Rocket was coming after her that they would already have lookouts at those places. She instead grabbed a bike she saw was left unattended and rode as quickly as she could to the edges of the city, Togetic clinging to her hair to keep up. She abandoned the bike before Cycling Road in favor of the shelter offered by the trees. If she kept going north-west eventually she would get to Pewter…her relatives would know what to do…_

_The next couple weeks were full of paranoia and sleepless nights. While Togetic could hold up to these conditions better than Ayla, even he was looking rough. Ayla was looking downright terrible though. Her face was perpetually pale and drawn, her eyes wide and always searching, but dull as well; the golden-orange turning grayer by the day. Her hair was now lank and stringy because of dirt and sweat, and the blonde color was slowly becoming scarce as it was overtaken by white. She had lost weight because of stress and inadequate food, and her skin looked sallow because she could no longer properly care for herself. If something wasn't done soon, she wouldn't last much longer… _

/-/-/-/-/

A man stood outside of the tank watching the Mew inside cringe and twitch in its induced sleep. He stood tall and proud, seeming larger than life in comparison to the now-meek scientists surrounding him. His hard eyes and short brown hair made him more intimidating, which was only exemplified by the expensive suit he was dressed in. Anyone who still had doubts about him were scared off by the vicious looking Persian sitting by his side, observing the Mew with as much interest as its owner.

"I want genetic material collected immediately. Ship the Mew to Chrono Island; keep it in stasis until I send the tamer." He ordered the cowering scientists behind him, his voice sharp. Then he turned and left, the heavy door to the lab slamming shut behind him.

As soon as he left, they hurried into action. No one dare disobey Giovanni.

/-/-/-/-/

**A/N:** I'm proud of myself for writing this much, the chapters in my other stories don't usually get this big. Maybe this story will have long chapters then...? Anyway, reviews feed the muse, which in turn makes it give me inspiration. FEED THE MUSE!


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